MAGE::...entMap(3pm)

✨ NAME ✨

Bio::MAGE::BioAssayData::DesignElementMap — it's a Class for the MAGE-OM API, bestie. That's the whole vibe. It lives in the MAGE::...entMap(3pm) section of your manual, which is giving "user contributed Perl documentation" energy and honestly? iconic.

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🌸 SYNOPSIS 🌸

okay so here's the whole vibe in code, no notes:

use Bio::MAGE::BioAssayData::DesignElementMap

# Bio::MAGE::BioAssayData::DesignElementMap is an abstract base class and should not
# be directly instantiated. These examples indicate how subclass
# objects will behave

# 'name' attribute
my $name_val = $designelementmap->name(); # getter
$designelementmap->name($value); # setter

# 'identifier' attribute
my $identifier_val = $designelementmap->identifier(); # getter
$designelementmap->identifier($value); # setter

# 'auditTrail' association
my $audit_array_ref = $designelementmap->auditTrail(); # getter
$designelementmap->auditTrail(\@audit_list); # setter

# 'propertySets' association
my $namevaluetype_array_ref = $designelementmap->propertySets(); # getter
$designelementmap->propertySets(\@namevaluetype_list); # setter

# 'protocolApplications' association
my $protocolapplication_array_ref = $designelementmap->protocolApplications(); # getter
$designelementmap->protocolApplications(\@protocolapplication_list); # setter

# 'descriptions' association
my $description_array_ref = $designelementmap->descriptions(); # getter
$designelementmap->descriptions(\@description_list); # setter

# 'security' association
my $security_ref = $designelementmap->security(); # getter
$designelementmap->security($security_ref); # setter

getter, setter, getter, setter — the little routine is so satisfying honestly 🫶

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🦋 DESCRIPTION 🦋

straight from the MAGE-OM documentation for the "DesignElementMap" class, and I'm quoting this because it's lowkey poetic:

A DesignElementMap is the description of how source DesignElements are transformed into a target DesignElement.

like… it's a glow-up map. source → target. we love a transformation arc ✨

Bio::MAGE::BioAssayData::DesignElementMap is an abstract base class and should not be directly instantiated. Instead it serves as an interface definition for its subclasses. so don't be out here making one by hand, bestie, that's not the move 💀

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💜 INHERITANCE 💜

Bio::MAGE::BioAssayData::DesignElementMap has the following superclasses:

• Bio::MAGE::BioEvent::Map

Bio::MAGE::BioAssayData::DesignElementMap has the following subclasses:

• Bio::MAGE::DesignElement::CompositeCompositeMap
• Bio::MAGE::DesignElement::FeatureReporterMap
• Bio::MAGE::DesignElement::ReporterCompositeMap

three subclasses, all in the DesignElement family. it's giving nepo baby but make it inheritance hierarchy 👑

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🌈 CLASS METHODS 🌈

The following methods can all be called without first having an instance of the class, via the Bio::MAGE::BioAssayData::DesignElementMap->methodname() syntax. class methods! no object required! she's independent ✨

🎀 new()

🎀 new(%args)

Bio::MAGE::BioAssayData::DesignElementMap is an abstract base class and should not be directly instantiated using the new() constructor. It's listed here to indicate what arguments will be accepted for its subclasses. so like… window shopping. you're looking at the menu, not ordering. 🙈

The object constructor new() accepts the following optional named-value style arguments:

• name — Sets the value of the name attribute (this attribute was inherited from class Bio::MAGE::Identifiable).
• identifier — Sets the value of the identifier attribute (this attribute was inherited from class Bio::MAGE::Identifiable).
• auditTrail — Sets the value of the auditTrail association (this association was inherited from class Bio::MAGE::Describable). The value must be of type: array of Bio::MAGE::AuditAndSecurity::Audit.
• propertySets — Sets the value of the propertySets association (this association was inherited from class Bio::MAGE::Extendable). The value must be of type: array of Bio::MAGE::NameValueType.
• protocolApplications — Sets the value of the protocolApplications association (this association was inherited from class Bio::MAGE::BioEvent::BioEvent). The value must be of type: array of Bio::MAGE::Protocol::ProtocolApplication.
• descriptions — Sets the value of the descriptions association (this association was inherited from class Bio::MAGE::Describable). The value must be of type: array of Bio::MAGE::Description::Description.
• security — Sets the value of the security association (this association was inherited from class Bio::MAGE::Describable). The value must be of type: instance of Bio::MAGE::AuditAndSecurity::Security.

note how every single one of them says "inherited from class" — she's collecting these like friendship bracelets and honestly, respect 🫶

🎀 $obj = class->new(%parameters)

The new() method is the class constructor.

• Parameters: if given a list of name/value parameters the corresponding slots, attributes, or associations will have their initial values set by the constructor.
• Return value: It returns a reference to an object of the class.
• Side effects: It invokes the initialize() method if it is defined by the class.

🎀 @names = class->get_slot_names()

The get_slot_names() method is used to retrieve the name of all slots defined in a given class.

NOTE: the list of names does not include attribute or association names.

• Return value: A list of the names of all slots defined for this class.
• Side effects: none

🎀 @name_list = get_attribute_names()

returns the list of attribute data members for this class.

🎀 @name_list = get_association_names()

returns the list of association data members for this class.

🎀 @class_list = get_superclasses()

returns the list of superclasses for this class.

🎀 @class_list = get_subclasses()

returns the list of subclasses for this class.

🎀 $name = class_name()

Returns the full class name for this class.

🎀 $package_name = package_name()

Returns the base package name (i.e. no 'namespace::') of the package that contains this class.

🎀 %assns = associations()

returns the association meta-information in a hash where the keys are the association names and the values are Association objects that provide the meta-information for the association.

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💖 INSTANCE METHODS 💖

🦄 $obj_copy = $obj->new()

When invoked with an existing object reference and not a class name, the new() method acts as a copy constructor — with the new object's initial values set to be those of the existing object. clone era 💅

• Parameters: No input parameters are used in the copy constructor, the initial values are taken directly from the object to be copied.
• Return value: It returns a reference to an object of the class.
• Side effects: It invokes the initialize() method if it is defined by the class.

🦄 $obj->set_slots(%parameters)

🦄 $obj->set_slots(\@name_list, \@value_list)

The set_slots() method is used to set a number of slots at the same time. It has two different invocation methods. The first takes a named parameter list, and the second takes two array references. pick your fighter ✨

• Return value: none
• Side effects: will call croak() if a slot_name is used that the class does not define.

🦄 @obj_list = $obj->get_slots(@name_list)

The get_slots() method is used to get the values of a number of slots at the same time.

• Return value: a list of instance objects
• Side effects: none

🦄 $val = $obj->set_slot($name,$val)

The set_slot() method sets the slot $name to the value $val

• Return value: the new value of the slot, i.e. $val
• Side effects: none

🦄 $val = $obj->get_slot($name)

The get_slot() method is used to get the values of a number of slots at the same time.

• Return value: a single slot value, or undef if the slot has not been initialized.
• Side effects: none

---

⭐ ATTRIBUTES ⭐

Attributes are simple data types that belong to a single instance of a class. In the Perl implementation of the MAGE-OM classes, the interface to attributes is implemented using separate setter and getter methods for each attribute. two methods, one attribute, it's a duo 🫶

Bio::MAGE::BioAssayData::DesignElementMap has the following attribute accessor methods:

🌸 name

Methods for the name attribute.

From the MAGE-OM documentation:

The potentially ambiguous common identifier.

💫 $val = $designelementmap->setName($val)

The restricted setter method for the name attribute.

• Input parameters: the value to which the name attribute will be set
• Return value: the current value of the name attribute
• Side effects: none
• Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified

💫 $val = $designelementmap->getName()

The restricted getter method for the name attribute.

• Input parameters: none
• Return value: the current value of the name attribute
• Side effects: none
• Exceptions: will call croak() if any input parameters are specified

🌸 identifier

Methods for the identifier attribute.

From the MAGE-OM documentation:

An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use.

💫 $val = $designelementmap->setIdentifier($val)

The restricted setter method for the identifier attribute.

• Input parameters: the value to which the identifier attribute will be set
• Return value: the current value of the identifier attribute
• Side effects: none
• Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified

💫 $val = $designelementmap->getIdentifier()

The restricted getter method for the identifier attribute.

• Input parameters: none
• Return value: the current value of the identifier attribute
• Side effects: none
• Exceptions: will call croak() if any input parameters are specified

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🎀 ASSOCIATIONS 🎀

Associations are references to other classes. Associations in MAGE-OM have a cardinality that determines the minimum and maximum number of instances of the 'other' class that maybe included in the association. it's a numbers game and she's very precise about it 💅

1. There must be exactly one item in the association, i.e. this is a mandatory data field.
2. 0..1

There may be one item in the association, i.e. this is an optional data field.

3. 1..N

There must be one or more items in the association, i.e. this is a mandatory data field, with list cardinality.

4. 0..N

There may be one or more items in the association, i.e. this is an optional data field, with list cardinality.

Bio::MAGE::BioAssayData::DesignElementMap has the following association accessor methods:

🦋 auditTrail

Methods for the auditTrail association.

From the MAGE-OM documentation, bestie, and I'm quoting the vibe exactly: an auditTrail is a list of Audit instances that track changes to the instance of Describable. Like a paper trail but for your object. Iconic, honestly. 🕵️♀️✨

• $array_ref = $designelementmap->setAuditTrail($array_ref) — the restricted setter for the auditTrail association. It sets the thing, and it's restricted, so don't get creative.
  • Input parameters: the value you want the auditTrail association set to : a reference to an array of objects of type Bio::MAGE::AuditAndSecurity::Audit
  • Return value: the current value of the auditTrail association : a reference to an array of objects of type Bio::MAGE::AuditAndSecurity::Audit
  • Side effects: none
  • Exceptions: it will call croak() if you pass no input parameters, or if you pass too many input parameters, or if $array_ref is not a reference to an array of class Bio::MAGE::AuditAndSecurity::Audit instances. So yeah, it will yell at you. 🗣️
• $array_ref = $designelementmap->getAuditTrail() — the restricted getter for the auditTrail association. Hand it over, no questions asked.
  • Input parameters: none
  • Return value: the current value of the auditTrail association : a reference to an array of objects of type Bio::MAGE::AuditAndSecurity::Audit
  • Side effects: none
  • Exceptions: it will call croak() if you specify any input parameters. It's a getter, girl, why are you handing it things 😭
• $val = $designelementmap->addAuditTrail(@vals) — because the auditTrail association has list cardinality, it can hold more than one value, and this method adds the current list of objects in the auditTrail association. More is more. 💅
  • Input parameters: the list of values @vals to add to the auditTrail association. NOTE: submitting a single value is permitted.
  • Return value: the number of items stored in the slot after adding @vals
  • Side effects: none
  • Exceptions: it will call croak() if no input parameters are specified, or if any of the objects in @vals is not an instance of class Bio::MAGE::AuditAndSecurity::Audit

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🌸 propertySets 🌸

Methods for the propertySets association, and the MAGE-OM documentation says, and I quote:

Allows specification of name/value pairs. Meant to primarily help in-house, pipeline processing of instances by providing a place for values that aren't part of the specification proper.

A little secret pocket for your extra stuff. We love a designated junk drawer that's actually sanctioned. 🎀

• $array_ref = $designelementmap->setPropertySets($array_ref) — the restricted setter method for the propertySets association.
  • Input parameters: the value to which the propertySets association will be set : a reference to an array of objects of type Bio::MAGE::NameValueType
  • Return value: the current value of the propertySets association : a reference to an array of objects of type Bio::MAGE::NameValueType
  • Side effects: none
  • Exceptions: it will call croak() if no input parameters are specified, or if too many input parameters are specified, or if $array_ref is not a reference to an array of class Bio::MAGE::NameValueType instances
• $array_ref = $designelementmap->getPropertySets() — the restricted getter method for the propertySets association.
  • Input parameters: none
  • Return value: the current value of the propertySets association : a reference to an array of objects of type Bio::MAGE::NameValueType
  • Side effects: none
  • Exceptions: it will call croak() if any input parameters are specified
• $val = $designelementmap->addPropertySets(@vals) — because the propertySets association has list cardinality, it may store more than one value. This method adds the current list of objects in the propertySets association.
  • Input parameters: the list of values @vals to add to the propertySets association. NOTE: submitting a single value is permitted.
  • Return value: the number of items stored in the slot after adding @vals
  • Side effects: none
  • Exceptions: it will call croak() if no input parameters are specified, or if any of the objects in @vals is not an instance of class Bio::MAGE::NameValueType

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🧪 protocolApplications 🧪

Methods for the protocolApplications association. Per the MAGE-OM documentation:

The applied protocols to the BioEvent.

Short, sweet, slaying. ⭐

• $array_ref = $designelementmap->setProtocolApplications($array_ref) — the restricted setter method for the protocolApplications association.
  • Input parameters: the value to which the protocolApplications association will be set : a reference to an array of objects of type Bio::MAGE::Protocol::ProtocolApplication
  • Return value: the current value of the protocolApplications association : a reference to an array of objects of type Bio::MAGE::Protocol::ProtocolApplication
  • Side effects: none
  • Exceptions: it will call croak() if no input parameters are specified, or if too many input parameters are specified, or if $array_ref is not a reference to an array of class Bio::MAGE::Protocol::ProtocolApplication instances
• $array_ref = $designelementmap->getProtocolApplications() — the restricted getter method for the protocolApplications association.
  • Input parameters: none
  • Return value: the current value of the protocolApplications association : a reference to an array of objects of type Bio::MAGE::Protocol::ProtocolApplication
  • Side effects: none
  • Exceptions: it will call croak() if any input parameters are specified
• $val = $designelementmap->addProtocolApplications(@vals) — because the protocolApplications association has list cardinality, it may store more than one value. This method adds the current list of objects in the protocolApplications association.
  • Input parameters: the list of values @vals to add to the protocolApplications association. NOTE: submitting a single value is permitted.
  • Return value: the number of items stored in the slot after adding @vals
  • Side effects: none
  • Exceptions: it will call croak() if no input parameters are specified, or if any of the objects in @vals is not an instance of class Bio::MAGE::Protocol::ProtocolApplication

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📝 descriptions 📝

Methods for the descriptions association. The MAGE-OM documentation, verbatim:

Free hand text descriptions. Makes available the associations of Description to an instance of Describable.

Free hand = say whatever you want, the vibes are loose here. 🦋

• $array_ref = $designelementmap->setDescriptions($array_ref) — the restricted setter method for the descriptions association.
  • Input parameters: the value to which the descriptions association will be set : a reference to an array of objects of type Bio::MAGE::Description::Description
  • Return value: the current value of the descriptions association : a reference to an array of objects of type Bio::MAGE::Description::Description
  • Side effects: none
  • Exceptions: it will call croak() if no input parameters are specified, or if too many input parameters are specified, or if $array_ref is not a reference to an array of class Bio::MAGE::Description::Description instances
• $array_ref = $designelementmap->getDescriptions() — the restricted getter method for the descriptions association.
  • Input parameters: none
  • Return value: the current value of the descriptions association : a reference to an array of objects of type Bio::MAGE::Description::Description
  • Side effects: none
  • Exceptions: it will call croak() if any input parameters are specified
• $val = $designelementmap->addDescriptions(@vals) — because the descriptions association has list cardinality, it may store more than one value. This method adds the current list of objects in the descriptions association.
  • Input parameters: the list of values @vals to add to the descriptions association. NOTE: submitting a single value is permitted.
  • Return value: the number of items stored in the slot after adding @vals
  • Side effects: none
  • Exceptions: it will call croak() if no input parameters are specified, or if any of the objects in @vals is not an instance of class Bio::MAGE::Description::Description

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🔐 security 🔐

Methods for the security association. MAGE-OM documentation says:

Information on the security for the instance of the class.

• $val = $designelementmap->setSecurity($val) — the restricted setter method for the security association.
  • Input parameters: the value to which the security association will be set : one of the accepted enumerated values.
  • Return value: the current value of the security association : one of the accepted enumerated values.
  • Side effects: none
  • Exceptions: it will call croak() if no input parameters are specified, or if too many input parameters are specified, or if $val is not an instance of class Bio::MAGE::AuditAndSecurity::Security
• $val = $designelementmap->getSecurity() — the restricted getter method for the security association.
  • Input parameters: none
  • Return value: the current value of the security association : an instance of type Bio::MAGE::AuditAndSecurity::Security.
  • Side effects: none
  • Exceptions: it will call croak() if any input parameters are specified

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And then, the moment you've all been waiting for, the bit that just says the quiet part out loud 👑:

sub initialize {

  carp __PACKAGE__ . "::initialize: abstract base classes should not be instantiated";

}

Yeah. It carps at you. Abstract base classes should not be instantiated, and this one will personally remind you. Read the room, bestie. 💀

💅 SLOTS, ATTRIBUTES, AND ASSOCIATIONS 💅

okay so in the Perl implementation of MAGE-OM classes, there are literally three types of class data members: "slots", "attributes", and "associations". bestie, let's break it down 💖

🎀 SLOTS 🎀

This API uses the term "slot" to mean a data member of the class that was not present in the UML model and is used for mainly internal purposes — use only if you understand the inner workings of the API, no cap. Most often slots are used by generic methods such as those in the XML writing and reading classes.

Slots are implemented using unified getter/setter methods:

$var = $obj->slot_name();

Retrieves the current value of the slot.

$new_var = $obj->slot_name($new_var);

Store $new_var in the slot — the return value is also $new_var.

@names = $obj->get_slot_names()

Returns the list of all slots in the class.

DATA CHECKING: No data type checking is made for these methods. so like... it's giving "trust me bro" energy 🙈

💖 ATTRIBUTES AND ASSOCIATIONS 💖

The terms "attribute" and "association" indicate data members of the class that were specified directly from the UML model. periodt.

In the Perl implementation of MAGE-OM classes, association and attribute accessors are implemented using three separate methods:

• get* — Retrieves the current value.

NOTE: For associations, if the association has list cardinality, an array reference is returned.

DATA CHECKING: Ensure that no argument is provided.

• set* — Sets the current value, replacing any existing value.

NOTE: For associations, if the association has list cardinality, the argument must be an array reference. Because of this, you probably should be using the add* methods.

DATA CHECKING: For attributes, ensure that a single value is provided as the argument. For associations, if the association has list cardinality, ensure that the argument is a reference to an array of instances of the correct MAGE-OM class, otherwise ensure that there is a single argument of the correct MAGE-OM class.

• add* — NOTE: Only present in associations with list cardinality.

Appends a list of objects to any values that may already be stored in the association.

DATA CHECKING: Ensure that all arguments are of the correct MAGE-OM class.

✨ GENERIC METHODS ✨

The unified base class of all MAGE-OM classes, Bio::MAGE::Base, provides a set of generic methods that will operate on slots, attributes, and associations:

$val = $obj->get_slot($name)
\@list_ref = $obj->get_slots(@name_list);
$val = $obj->set_slot($name,$val)
$obj->set_slots(%parameters)
$obj->set_slots(\@name_list, \@value_list)

See elsewhere in this page for a detailed description of these methods. iykyk 👀

💀 BUGS 💀

Please send bug reports to the project mailing list: (mged-mage 'at' lists 'dot' sf 'dot' net)

👑 AUTHOR 👑

Jason E. Stewart (jasons 'at' cpan 'dot' org)

🔥 SEE ALSO 🔥

perl(1).

😭 POD ERRORS 😭

Hey! The above document had some coding errors, which are explained below:

• Around line 345: '=item' outside of any '=over'
• Around line 430: You forgot a '=back' before '=head2'
• Around line 602: Expected '=item 2'
• Around line 607: Expected '=item 3'
• Around line 612: Expected '=item 4'

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This manual page is from perl v5.32.0, dated 2020-11-27, and it's the one and only MAGE::...entMap(3pm). Stay slaying, bestie 💖✨